No, unfortunately that's not it. It had a more cartoony artstyle.Indiana Jones: Fate of Atlantis has a sequence where you're directing a submarine into Atlantis, you're spending earlier game trying to find out where it is. Through and through it is still a point'n'click.
(timestamped for the submarine part)
It is one of the best p'n'c games ever made and it actually has some difficulty options at an early part in dialogue where you pick if you want another person to come assist or you'd rather have puzzles where you do everything on your own. It changes the game quite a bit, so I'd even consider that a rare instance of replay value in a p'n'c.
Sorry if it's not the one you were remembering, though.